Biodiversity Community Integrated Knowledge Library

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Project logo, marketing pack and website design and development

Project logo marketing pack and website design and development

Plan for dissemination and exploitation of project results
Best practice manual for findability, re-use and accessibility of infrastructures

Best practice manual for findability reuse and accessibility of infrastructures

User requirements analysis report
Recommendations for interoperability among infrastructures
Stakeholder input into the network graph provided by Third Global Biodiversity Informatics Conference (GBIC3)

Stakeholder input into the network graph provided by Third Global Biodiversity Informatics Conference GBIC3

Architecture Design for a pan-European PID system for Digital Specimens
Search and link association services: A RESTful API, which will input a link/accession number and return a ranked list of neighbors links with a confidence score

Search and link association services: A RESTful API, which will input a link/accessionnumber and return a ranked list of neighbors links with a confidence score

Passage retrieval services: A RESTful API, which will input a set of keywords and return a set of articles/passages ranked by relevance

Validation tool open-source software release
Relational network graph for the Biodiversity Knowledge Hub (BKH)
Availability via API of single, harmonised sequenced material source annotations in ENA
Web interface for ELIXIR Contextual Data Clearinghouse
Web visualisation of mappings between CoL and other checklists
A workflow for bi-directional linking of data from literature to external resources
Validation and curation workbench for taxonomic data
Evaluation benchmark: a database of questions associated with a set of relevant articles (e.g. PMIDs) to measure the progress of the WP towards an effective search service

Evaluation benchmark: a database of questions associated with a set of relevant articles(e.g. PMIDs) to measure the progress of the WP towards an effective search service

Applications for interoperable access to OpenBiodiv through semantically enhanced queries

Project call definition and execution plan, published via BiCIKL website

Project call definition and execution plan published via BiCIKL website

Data Management Plan

Publications

Ukrainian Plant Trait Database: UkrTrait v. 1.0

Auteurs: Vynokurov D, Borovyk D, Chusova O et al.
Publié dans: Biodiversity Data Journal, Numéro 12, 2024, Page(s) e118128, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.12.e118128

Envisaging a global infrastructure to exploit the potential of digitised collections

Auteurs: Groom Q, Dillen M, Addink W et al.
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e109439, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e109439

A comprehensive database of squirrel distribution and occurrence in South Asia

Auteurs: Swati U, D`Souza S, Aravind PS et al.
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e109946, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e109946

The European Nucleotide Archive in 2021.

Auteurs: Carla Cummins; Alisha Ahamed; Raheela Aslam; Josephine Burgin; Rajkumar Devraj; Ossama Edbali; Dipayan Gupta; Peter W. Harrison; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Balavenkataraman Kadhirvelu; Simon Kay; Manish Kumar; Ankur Lathi; Rasko Leinonen; Fábio Madeira; Nandana Madhusoodanan; Milena Mansurova; Colman O’Cathail; Matt Pearce; Stephane P
Publié dans: Nucleic Acids Research, Numéro 50, 2022, Page(s) D106-D110, ISSN 1362-4954
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkab1051

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Auteurs: Abarenkov K, Nilsson R, Larsson K et al.
Publié dans: Nucleic Acids Research, Numéro 52, 2024, Page(s) D791–D797, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad1039

The comprehensive checklist of myxomycetes of Ukraine, based on extended occurrence and reference datasets

Auteurs: Yatsiuk I, Leshchenko Y, Viunnyk V et al.
Publié dans: Biodiversity Data Journal, Numéro 12, 2024, Page(s) e120891, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.12.e120891

Paying it forward: Crowdsourcing the harmonisation and linking of taxon names and biodiversity identifiers

Auteurs: Seah BKB
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e114076, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e114076

Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park

Auteurs: Kermek D, Pischiutta N, Hlebec D et al.
Publié dans: Biodiversity Data Journal, Numéro 12, 2024, Page(s) e121398, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.12.e121398

The MOBIOS+: A FAIR (Findable, Accessible, Interoperable and Reusable) database for Mindanao's terrestrial biodiversity

Auteurs: Tanalgo KC, Dela Cruz KC, Agduma AR et al.
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e110016, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e110016

An annotated nomenclatural checklist of endemic vascular plants distributed in the Ukrainian Carpathians

Auteurs: Novikov A
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e10392, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e103921

Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people

Auteurs: Page R
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e107914, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e107914

Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability

Auteurs: Meyer R, Appeltans W, Duncan W et al.
Publié dans: Biodiversity Data Journal, Numéro 11, 2023, Page(s) e112420, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.11.e112420

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Auteurs: Waterhouse RM, Adam-Blondon AF, Agosti D et al.
Publié dans: F1000Research, Numéro 10, 2021, Page(s) 1238, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.73825.1

Microbial diversity in four Mediterranean irciniid sponges

Auteurs: Skaraki K, Pavloudi C, Dailianis T et al.
Publié dans: Biodiversity Data Journal, Numéro 12, 2024, Page(s) e114809, ISSN 1314-2828
Éditeur: Pensoft Publishers
DOI: 10.3897/bdj.12.e114809

ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data

Auteurs: Gupta, Vikas; Paupério, Joana; Burgin, Josephine; Jayathilaka, Suran; Cochrane, Guy
Publié dans: F1000Research, Numéro 11, 2022, Page(s) 1042, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.123934.1

The ENA Source Attribute Helper: An API for improved biological source data

Auteurs: Gupta V, Paupério J, Burgin J, Jayathilaka S, Cochrane G
Publié dans: Biodiversity Information Science and Standards 6, Numéro 6, 2022, Page(s) e91118
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91118

The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data

Auteurs: Penev L, Kureas D, Groom Q et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e111482
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.111482

Towards Connecting Molecular Data and the Biodiversity Research Community: An ENA and ELIXIR biodiversity community perspective

Auteurs: Paupério J, Burgin J, Gabaldón T, Lanfear J, Waterhouse RM, Cochrane G
Publié dans: Biodiversity Information Science and Standards, Numéro 6, 2022, Page(s) e91204
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91204

Biodiversity Literature Repository: Building the customized FAIR repository by using custom metadata

Auteurs: Ioannidis-Pantopikos A, Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75147
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75147

TreatmentBank: Plazi’s strategies and its implementation to most efficiently liberate data from scholarly publications

Auteurs: Guidoti M, Sokolowicz C, Simoes F, Gonçalves V, Ruschel T, Alvares DJ, Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75690
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75690

The TreatmentBank factory: Data access

Auteurs: Agosti, Donat; Miller, Jeremy
Publié dans: Numéro 1, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7262609

Linking and the Role of the Material Citation

Auteurs: Miller JA, Agosti D, Guidoti M, Rivera Quiroz F
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75543
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75543

A Possible Workflow from New and Legacy Publications to keep the World Flora Online up to date with New Species and Augmenting Taxonomic Treatments

Auteurs: Agosti D, Benichou L, Penev L, Hyam R
Publié dans: Biodiversity Information Science and Standards, Numéro 6, 2022, Page(s) e91241
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91241

Enabling Published Taxonomic Data to be used to Address the Biodiversity Crisis: Biodiversity Literature Repository and TreatmentBank

Auteurs: Donat Agosti; Patrick Ruch; Jose Benito Gonzalez Lopez; Lyubomir Penev
Publié dans: Biodiversity Information Science and Standards 6: e91167, Numéro 6, 2022
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91167

The significance of taxonomic publications to understand biodiversity in the digital world

Auteurs: Agosti, Donat
Publié dans: Numéro 1, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7081339

The BHL-Plazi Partnership: Getting data from the 1800s directly into 21st century, reused digital accessible knowledge

Auteurs: Alvares DJ, Guidoti M, Simoes F, Sokolowicz C, Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75604
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75604

Connecting the Dots: Joint development of best practices between infrastructures in support of bidirectional data linking

Auteurs: Wouter Addink; Niki Kyriakopoulou
Publié dans: Biodiversity Information Science and Standards, Numéro 6, 2022, Page(s) e91428
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91428

Pre-Publication Data Linking in Taxonomy and Biodiversity: The ARPHA and Metotaxa-Metostem Publishing Systems.

Auteurs: Benichou L, Salaün M, Boyadzhieva I et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e110919
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.110919

"Towards ""Biodiversity PMC"""

Auteurs: Pasche E, Agosti D, Penev L et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e111647
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.111647

Discovering known biodiversity

Auteurs: Agosti, Donat
Publié dans: Numéro 1, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6574848

Delivering Fit-for-Use Data: Quality control

Auteurs: Simoes F, Agosti D, Guidoti M
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75432
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75432

Improving FAIRness of eDNA and Metabarcoding Data: Standards and tools for European Nucleotide Archive data deposition

Auteurs: Paupério J, Gupta V, Burgin J et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e111835
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.111835

Beyond the print and PDF prisons: Data about biodiversity want to be free

Auteurs: Agosti, Donat
Publié dans: Numéro 1, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6777916

The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, PENSOFT, MNHN, CETAF, Zenodo, and SIBiLS

Auteurs: Agosti D, Penev L, Ruch P et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e110681
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.110681

Zen and the Art of Persistent Identifier Service Development for Digital Specimen

Auteurs: Islam S, Theocharides S, Addink W
Publié dans: Biodiversity Information Science and Standards, Numéro 6, 2022, Page(s) e91168
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91168

(Re)Discovering Known Biodiversity: Introduction

Auteurs: Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75491
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75491

Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective

Auteurs: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Barov B, Hobern D, Banki O, Addink W, Kõljalg U, Ruch P, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) 3
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.74233

Hacking Infrastructures Together: Towards better interoperability of infrastructures

Auteurs: Meeus S, Addink W, Agosti D, Arvanitidis C, Dimitrova M, González-Aranda JM, Holetschek J, Islam S, Jeppesen TS, Mietchen D, Robertson T, Sanchez Cano FM, Trekels M, Groom Q
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e74325
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.74325

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Auteurs: Abarenkov K, Zirk A, Põldmaa K, Piirmann T, Pöhönen R, Ivanov F, Adojaan K, Kõljalg U
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e74249
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.74249

Synospecies, an application to reflect changes in taxonomic names based on a triple store based on taxonomic data liberated from publication

Auteurs: Gmür R, Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e75641
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.75641

From SIBiLS to Biodiversity PMC: Foundations for the One Health Library

Auteurs: Pasche E, Gobeill J, Agosti D et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e111660
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.111660

The OpenBiodiv Knowledge Graph Rebuilt: A semantic hub on top of the ARPHA-published content and the Biodiversity Literature Repository

Auteurs: Penev L, Dimitrova M, Zhelezov G, Georgiev T
Publié dans: Biodiversity Information Science and Standards, Numéro 6, 2022, Page(s) e91357
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.6.91357

Discovering Known Biodiversity: Digital accessible knowledge — Getting the community involved

Auteurs: Sokolowicz C, Guidoti M, Agosti D
Publié dans: Biodiversity Information Science and Standards, Numéro 5, 2021, Page(s) e74369
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.5.74369

Nothing in (taxonomic) publishing makes sense except in the light of treatments

Auteurs: Agosti, Donat
Publié dans: Numéro 1, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6590938

Nanopublications for Biodiversity Go Live

Auteurs: Penev L, Kuhn T, Pyle R et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023, Page(s) e110725
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.110725

OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph

Auteurs: Penev L, Zhelezov G, Dimitrova M et al.
Publié dans: Biodiversity Information Science and Standards, Numéro 7, 2023
Éditeur: Pensoft Publishers
DOI: 10.3897/biss.7.110724

Joint statement by CETAF, SPNHC and BHL on DATA within scientific publications: clarification of [non]copyrightability

Auteurs: Benichou L, Agosti D, Egloff W et al.
Publié dans: Research Ideas and Outcomes, Numéro 9, 2023, Page(s) e115466, ISSN 2367-7163
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.9.e115466

Global access to nomenclatural botanical resources: Evaluating open access availability

Auteurs: Nicolson N, Trekels M, Groom Q et al.
Publié dans: Plants, People, Planet, Numéro 5, 2023, Page(s) 899-907, ISSN 2572-2611
Éditeur: New Phytologist Foundation
DOI: 10.1002/ppp3.10438

Recommendations for interoperability among infrastructures

Auteurs: Meeus S, Addink W, Agosti D et al.
Publié dans: Research Ideas and Outcomes, Numéro 8, 2022, Page(s) e96180, ISSN 2367-7163
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.8.e96180

Liberate the power of biodiversity literature as FAIR digital objects

Auteurs: Agosti D, Bénichou L, Casino A et al.
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, Page(s) e126586
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.10.e126586

Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing

Auteurs: Donat Agosti; Laurence Benichou; Wouter Addink; Christos Arvanitidis; Terence Catapano; Guy Cochrane; Mathias Dillen; Markus Döring; Teodor Georgiev; Isabelle Gérard; Quentin Groom; Puneet Kishor; Andreas Kroh; Jiří Kvaček; Patricia Mergen; Daniel Mietchen; Joana Pauperio; Guido Sautter; Lyubomir Penev
Publié dans: Research Ideas and Outcomes, Numéro 8, 2022, Page(s) e97374
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.8.e97374

Network analysis of specimen co-collection

Auteurs: Meeus S, August T, Trekels M, Reyserhove L, & Groom QJ
Publié dans: BioHackrXiv Preprints, 2021
Éditeur: BioHackrXiv Preprints
DOI: 10.37044/osf.io/4ahng

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Auteurs: Benichou L, Buschbom J, Campbell M, Hermann E, Kvacek J, Mergen P, Mitchell L, Rinaldo C, Agosti D
Publié dans: Research Ideas and Outcomes, Numéro 10, 2022, Page(s) 1-7
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.8.e94338

Uniting FAIR data through interlinked, machine-actionable infrastructures

Auteurs: Penev L, Groom Q, Casino A et al.
Publié dans: Research Ideas and Outcomes, Numéro 10, 2024, Page(s) e126588
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.10.e126588

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